ArticleBMC genomics2014
funRNA: a fungi-centered genomics platform for genes encoding key components of RNAi.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
16 citing papers in PubMed, 63 citations in OpenAlex.
- Clade-wide fungal proteome analysis reveals structure-function conservation in divergent Dicer proteins.Computational and structural biotechnology journal · 2025Article
- Harnessing RNA interference for the control of Fusarium species: A critical review.Molecular plant pathology · 2024Review
- Gene Silencing via RNA Interference in Cryptococcus.Methods in molecular biology (Clifton, N.J.) · 2024Article
- MicroRNA-like RNA Functions Are Required for the Biosynthesis of Active Compounds in the Medicinal FungusMicrobiology spectrum · 2022Article
- Comprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved links.eLife · 2022Article
- Discovery of microRNA-like Small RNAs in Pathogenic Plant FungusInternational journal of molecular sciences · 2022Article
- The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation.BMC biology · 2021Article
- The Evolutionary Significance of RNAi in the Fungal Kingdom.International journal of molecular sciences · 2020Review
- Identification and characterization of Dicer-like genes in leaf rust pathogen (Puccinia triticina) of wheat.Functional & integrative genomics · 2020Article
- RNA interference core components identified and characterised in Verticillium nonalfalfae, a vascular wilt pathogenic plant fungi of hops.Scientific reports · 2019Article
- Discovery and profiling of small RNAs from Puccinia triticina by deep sequencing and identification of their potential targets in wheat.Functional & integrative genomics · 2019Article
- Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungusPeerJ · 2018Article
- Cut-and-Paste Transposons in Fungi with Diverse Lifestyles.Genome biology and evolution · 2017Article
- RNAi-Based Functional Genomics Identifies New Virulence Determinants in Mucormycosis.PLoS pathogens · 2017Article
- Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense.Scientific reports · 2015Article
- InCoB2014: mining biological data from genomics for transforming industry and health.BMC genomics · 2014Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA interference (RNAi) is involved in genome defense as well as diverse cellular, developmental, and physiological processes. Key components of RNAi are Argonaute, Dicer, and RNA-dependent RNA polymerase (RdRP), which have been functionally characterized mainly in model organisms. The key components are believed to exist throughout eukaryotes; however, there is no systematic platform for archiving and dissecting these important gene families. In addition, few fungi have been studied to date, limiting our understanding of RNAi in fungi. Here we present funRNA http://funrna.riceblast.snu.ac.kr/, a fungal kingdom-wide comparative genomics platform for putative genes encoding Argonaute, Dicer, and RdRP. DESCRIPTION: To identify and archive genes encoding the abovementioned key components, protein domain profiles were determined from reference sequences obtained from UniProtKB/SwissProt. The domain profiles were searched using fungal, metazoan, and plant genomes, as well as bacterial and archaeal genomes. 1,163, 442, and 678 genes encoding Argonaute, Dicer, and RdRP, respectively, were predicted. Based on the identification results, active site variation of Argonaute, diversification of Dicer, and sequence analysis of RdRP were discussed in a fungus-oriented manner. funRNA provides results from diverse bioinformatics programs and job submission forms for BLAST, BLASTMatrix, and ClustalW. Furthermore, sequence collections created in funRNA are synced with several gene family analysis portals and databases, offering further analysis opportunities.
conclusionsfunRNA provides identification results from a broad taxonomic range and diverse analysis functions, and could be used in diverse comparative and evolutionary studies. It could serve as a versatile genomics workbench for key components of RNAi.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.